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I have a 1990 and 1992 Ford F150 5.0 that I'm swapping motors. The 1992 motor locked up so I'm putting the motor from the 1990 into the 1992. I've pretty much got that done but the wiring harness for the 2 distributor shafts are different. Now I'm trying to put the distributor shaft from the 1990 onto the 1992 and the #1 spark plug is not firing. I checked the coil with a test light by turning the key on and off and it showed 2 positive wires light up but the negative wires also lit up (is something not grounded or do I need to run a second ground)
That is the distributor modules job, to ground the coil. That is how the coil makes spark. It has power all the time on the + side with the key on, and the negative side is grounded and ungrounded at the right time to fire the sparkplugs.
Not sure why the 1990 distributor did not just plug in. Unless the 1992 had a remote mounted module.
The picture below is the earlier setup that Ford used. The ignition module that turns the coil on and off is mounted directly to the distributor, it's the rectangle grey looking piece that is bolted to it and the wires plug into. They had problems with them getting too hot, so later on they moved the module off the dist and mounted it somewhere in the engine bay on a heat sink.
So I am assuming you just swapped the whole complete distributor? That should get you going, if you get it in the engine correctly Put your testlight or voltmeter on negative of the coil like you did before. You got 12v on the negative. As you crank the engine over, the testlight or voltmeter should start blinking, that is the module turning the coil on and off.
If I were you I would swap what I could off the newer engine onto the older engine. There are some sensors that are probably in different places, and the later engine might even be mass air, you will need to swap all that over also. Just swap the entire top dress of the bad engine onto the good engine.